NPASS Compound

Structure

NPC211920 OpenBabel07101718292D 42 47 0 0 1 0 0 0 0 0999 V2000 0.8660 -4.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8660 -3.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.7321 -2.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8660 -0.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.1962 -4.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.3301 -4.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.1962 -3.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.7321 -4.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.5981 1.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8660 -4.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.4641 -4.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.3301 -2.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.5981 0.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.7321 -3.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.4641 2.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.7321 -0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.0570 1.0878 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.3301 0.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.6750 1.0878 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.0000 -4.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.4641 -3.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.4641 -0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8660 -2.5000 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -1.7321 -1.0000 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -0.3660 2.0388 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8660 -1.5000 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 0.8660 -2.5000 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 2.5981 -2.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.4641 -1.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.0000 -3.0000 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -0.8660 -1.5000 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 0.0000 -1.0000 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -0.8660 0.5000 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -4.3301 1.5000 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 0.2218 2.8479 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1.7321 -1.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 2.5981 -1.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -4.3301 -1.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.3660 2.0388 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -2.5981 -1.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1.7321 -3.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.0000 -0.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1 20 2 0 0 0 0 3 31 1 0 0 0 0 5 6 2 0 0 0 0 5 7 1 0 0 0 0 6 11 1 0 0 0 0 7 12 2 0 0 0 0 8 10 1 0 0 0 0 8 14 1 0 0 0 0 9 13 2 0 0 0 0 9 15 1 0 0 0 0 10 20 1 0 0 0 0 11 21 2 0 0 0 0 12 21 1 0 0 0 0 13 22 1 0 0 0 0 14 23 1 0 0 0 0 15 34 2 0 0 0 0 16 24 1 0 0 0 0 17 25 1 0 0 0 0 17 33 1 0 0 0 0 18 22 2 0 0 0 0 18 34 1 0 0 0 0 19 33 1 0 0 0 0 19 39 1 0 0 0 0 20 30 1 0 0 0 0 21 28 1 0 0 0 0 22 29 1 0 0 0 0 23 30 1 6 0 0 0 23 31 1 0 0 0 0 24 31 1 1 0 0 0 24 40 1 0 0 0 0 25 35 2 0 0 0 0 25 39 1 0 0 0 0 26 27 1 0 0 0 0 26 32 1 1 0 0 0 26 36 1 0 0 0 0 27 30 1 6 0 0 0 27 41 1 0 0 0 0 28 37 2 0 0 0 0 28 41 1 0 0 0 0 29 38 2 0 0 0 0 29 40 1 0 0 0 0 30 2 1 6 0 0 0 31 32 1 6 0 0 0 32 4 1 6 0 0 0 32 42 1 0 0 0 0 33 16 1 1 0 0 0 33 42 1 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	575.25
Volume:	582.939
LogP:	3.751
LogD:	2.768
LogS:	-4.511
# Rotatable Bonds:	6
TPSA:	121.25
# H-Bond Aceptor:	9
# H-Bond Donor:	1
# Rings:	6
# Heavy Atoms:	9

MedChem Properties

QED Drug-Likeness Score:	0.32
Synthetic Accessibility Score:	5.389
Fsp3:	0.515
Lipinski Rule-of-5:	Accepted
Pfizer Rule:	Accepted
GSK Rule:	Rejected
BMS Rule:	0
Golden Triangle Rule:	Rejected
Chelating Alert:	0
PAINS Alert:	0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:	-5.391
MDCK Permeability:	3.2643329177517444e-05
Pgp-inhibitor:	0.99
Pgp-substrate:	0.004
Human Intestinal Absorption (HIA):	0.006
20% Bioavailability (F20%):	0.958
30% Bioavailability (F30%):	0.979

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.88
Plasma Protein Binding (PPB):	84.37376403808594%
Volume Distribution (VD):	1.502
Pgp-substrate:	9.83314037322998%

ADMET: Metabolism

CYP1A2-inhibitor:	0.178
CYP1A2-substrate:	0.136
CYP2C19-inhibitor:	0.421
CYP2C19-substrate:	0.1
CYP2C9-inhibitor:	0.435
CYP2C9-substrate:	0.07
CYP2D6-inhibitor:	0.225
CYP2D6-substrate:	0.057
CYP3A4-inhibitor:	0.959
CYP3A4-substrate:	0.371

ADMET: Excretion

Clearance (CL):	12.411
Half-life (T1/2):	0.601

ADMET: Toxicity

hERG Blockers:	0.865
Human Hepatotoxicity (H-HT):	0.137
Drug-inuced Liver Injury (DILI):	0.708
AMES Toxicity:	0.011
Rat Oral Acute Toxicity:	0.208
Maximum Recommended Daily Dose:	0.928
Skin Sensitization:	0.233
Carcinogencity:	0.174
Eye Corrosion:	0.003
Eye Irritation:	0.034
Respiratory Toxicity:	0.878

Download Data

Data Type	Select
General Info & Identifiers & Properties
Structure MOL file
Source Organisms
Biological Activities
Similar NPs/Drugs

Natural Product: NPC211920

Natural Product ID:	NPC211920
*Common Name:**	Scutehenanine C
IUPAC Name:	[(1S,3S,4aR,5S,6R,6aR,10aS,10bS)-6-benzoyloxy-5-hydroxy-4a,6a,10b-trimethyl-7-methylidene-2'-oxospiro[1,2,5,6,8,9,10,10a-octahydrobenzo[f]chromene-3,4'-oxolane]-1-yl] pyridine-3-carboxylate
Synonyms:	Scutehenanine C
Standard InCHIKey:	GMMYKYNDSYLONO-GRTFKUIQSA-N
Standard InCHI:	InChI=1S/C33H37NO8/c1-20-10-8-14-23-30(20,2)27(41-28(37)21-11-6-5-7-12-21)26(36)32(4)31(23,3)24(16-33(42-32)17-25(35)39-19-33)40-29(38)22-13-9-15-34-18-22/h5-7,9,11-13,15,18,23-24,26-27,36H,1,8,10,14,16-17,19H2,2-4H3/t23-,24-,26-,27-,30-,31-,32-,33-/m0/s1
SMILES:	C=C1CCC[C@H]2[C@@]1(C)[C@H]([C@@H]([C@@]1(C)[C@]2(C)[C@H](C[C@@]2(CC(=O)OC2)O1)OC(=O)c1cccnc1)O)OC(=O)c1ccccc1
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	CHEMBL1077450
PubChem CID:	44556949
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000012] Lipids and lipid-like molecules [CHEMONTID:0000259] Prenol lipids [CHEMONTID:0001283] Terpene lactones [CHEMONTID:0001538] Diterpene lactones

*Note: the InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
**Note: the Chemical Classification was calculated by NPClassifier Version 1.5. Reference: PMID:34662515.

Species Source

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Organism ID	Organism Name	Taxonomy Level	Family	SuperKingdom	Isolation Part	Collection Location	Collection Time	Reference
NPO16039	Scutellaria barbata	Species	Lamiaceae	Eukaryota	aerial parts	Seoul, Korea	n.a.	PMID[26331882]
NPO16039	Scutellaria barbata	Species	Lamiaceae	Eukaryota	whole plants	Nanning District, Guangxi Province, China	2012-Sep	PMID[25647077]
NPO16039	Scutellaria barbata	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[20078074]
NPO16039	Scutellaria barbata	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[19962306]
NPO16039	Scutellaria barbata	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[19785430]
NPO16039	Scutellaria barbata	Species	Lamiaceae	Eukaryota	n.a.	aerial part	n.a.	PMID[18239311]
NPO16039	Scutellaria barbata	Species	Lamiaceae	Eukaryota	n.a.	aerial part	n.a.	PMID[17666848]
NPO16039	Scutellaria barbata	Species	Lamiaceae	Eukaryota	n.a.	whole plant	n.a.	PMID[16755060]
NPO16039	Scutellaria barbata	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO16039	Scutellaria barbata	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]

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☑ Note for Reference:
In addition to directly collecting NP source organism data from primary literature (where reference will provided as NCBI PMID or DOI links), NPASS also integrated them from below databases:
☉ UNPD: Universal Natural Products Database [PMID: 23638153].
☉ StreptomeDB: a database of streptomycetes natural products [PMID: 33051671].
☉ TM-MC: a database of medicinal materials and chemical compounds in Northeast Asian traditional medicine [PMID: 26156871].
☉ TCM@Taiwan: a Traditional Chinese Medicine database [PMID: 21253603].
☉ TCMID: a Traditional Chinese Medicine database [PMID: 29106634].
☉ TCMSP: The traditional Chinese medicine systems pharmacology database and analysis platform [PMID: 24735618].
☉ HerDing: a herb recommendation system to treat diseases using genes and chemicals [PMID: 26980517].
☉ MetaboLights: a metabolomics database [PMID: 27010336].
☉ FooDB: a database of constituents, chemistry and biology of food species [www.foodb.ca].

NP Quantity Composition/Concentration

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Organism ID	NP ID	Organism Material Preparation	Organism Part	NP Quantity (Standard)	NP Quantity (Minimum)	NP Quantity (Maximum)	Quantity Unit	Reference
No data available in table

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☑ Note for Reference:
In addition to directly collecting NP quantitative data from primary literature (where reference will provided as NCBI PMID or DOI links), NPASS also integrated NP quantitative records for specific NP domains (e.g., NPS from foods or herbs) from domain-specific databases. These databases include:
☉ DUKE: Dr. Duke's Phytochemical and Ethnobotanical Databases.
☉ PHENOL EXPLORER: is the first comprehensive database on polyphenol content in foods [PMID: 24103452], its homepage can be accessed at here.
☉ FooDB: a database of constituents, chemistry and biology of food species [www.foodb.ca].

Biological Activity

Activity Type	# Activity
IC50	3

Activity Type	# Activity
Cell Line	2
NON-MOLECULAR	1

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Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference
NPT91	Cell Line	KB	Homo sapiens	IC50	=	2900.0	nM	PMID[484997]
NPT139	Cell Line	HT-29	Homo sapiens	IC50	=	5300.0	nM	PMID[484997]
NPT20529	NON-MOLECULAR	NON-PROTEIN TARGET	n.a.	IC50	=	3400.0	nM	PMID[484997]

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☑ Note for Activity Records:
☉ The quantitative biological activities were primarily integrated from ChEMBL (Version-30) database and were also directly collected from PubMed literature. PubMed PMID was provided as the reference link for each activity record.

Chemically structural similarity: I. Similar Active Natural Products in NPASS

Top-200 similar NPs were calculated against the active-NP-set (includes 4,3285 NPs with experimentally-derived bioactivity available in NPASS)

Similarity level is defined by Tanimoto coefficient (Tc) between two molecules. Tc lies between [0, 1] where '1' indicates the highest similarity. What is Tanimoto coefficient

● The left chart: Distribution of similarity level between NPC211920 and all remaining natural products in the NPASS database.
● The right table: Most similar natural products (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	350
0.1-0.2	1456
0.2-0.3	3135
0.3-0.4	9735
0.4-0.5	16937
0.5-0.6	8949
0.6-0.7	1835
0.7-0.8	115
0.8-0.85	51
0.85-0.9	53
0.9-0.95	63
0.95-1	18

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Similarity Score	Similarity Level	Natural Product ID
0.9901	High Similarity	NPC124029
0.9802	High Similarity	NPC477902
0.966	High Similarity	NPC477906
0.966	High Similarity	NPC150698
0.966	High Similarity	NPC96801

Showing 1 to 5 of 200 entries

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Chemically structural similarity: II. Similar Clinical/Approved Drugs

Similarity level is defined by Tanimoto coefficient (Tc) between two molecules.

● The left chart: Distribution of similarity level between NPC211920 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	230
0.1-0.2	536
0.2-0.3	704
0.3-0.4	1847
0.4-0.5	3358
0.5-0.6	2001
0.6-0.7	451
0.7-0.8	22
0.8-0.85	1
0.85-0.9	0
0.9-0.95	0
0.95-1	0

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Similarity Score	Similarity Level	Drug ID	Developmental Stage
0.813	Intermediate Similarity	NPD8468	Phase 2
0.791	Intermediate Similarity	NPD8304	Clinical (unspecified phase)
0.7767	Intermediate Similarity	NPD7396	Approved
0.7636	Intermediate Similarity	NPD7927	Clinical (unspecified phase)
0.7512	Intermediate Similarity	NPD5975	Clinical (unspecified phase)

Showing 1 to 5 of 200 entries

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Bioactivity similarity: Similar Natural Products in NPASS

Bioactivity similarity was calculated based on bioactivity descriptors of compounds. The bioactivity descriptors were calculated by a recently developed AI algorithm Chemical Checker (CC) [Nature Biotechnology, 38:1087–1096, 2020; Nature Communications, 12:3932, 2021], which evaluated bioactivity similarities at five levels:
☉ A: chemistry similarity;
☉ B: biological targets similarity;
☉ C: networks similarity;
☉ D: cell-based bioactivity similarity;
☉ E: similarity based on clinical data.

Those 5 categories of CC bioactivity descriptors were calculated and then subjected to manifold projection using UMAP algorithm, to project all NPs on a 2-Dimensional space. The current NP was highlighted with a small circle in the 2-D map. Below figures: left-to-right, A-to-E.

A: chemistry similarity

B: biological targets similarity

C: networks similarity

D: cell-based bioactivity similarity

E: similarity based on clinical data